My VCF file looks like the screenshot below and I believe it is missing the necessary fields to convert it into a genotype matrix that I can actually use. It's 14GB and contains 88 samples.
How can I fill the missing fields (e.g. GT) and convert it into a genotype matrix with exact commands?
I've found references for similar questions that are one sentence answers with a link to a tool but many issues aren't addressed and I have yet to find a good tutorial on how to fill in missing fields on a VCF file and convert it to genotype/SNPs matrix.
Thank you : )